I'm starting with virgo and I had a problem trying to start the server from eclipse. The container is started without problems but if I try to access localhost:8080 I get 404 error.
I am using the Virgo Jetty Server 3.0.2 and following the step by step to install the Virgo tooling.

The curious thing is that if I initialize the container from the command prompt it boots without problems and I can access localhost:8080

I could reproduce your setup. When starting VJS from the command line I can access the admin console via localhost:8080/admin.
When starting the VJS from within Eclipse there is no process listening on port 8080. I raised an issue https://bugs.eclipse.org/bugs/show_bug.cgi?id=369238.